Dr. Cara Gormally, a teaching faculty member in the School of Biology, along with research collaborators Peggy Brickman and Mary Lutz at the University of Georgia, have developed the Test of Scientific Literacy Skills (TOSLS)--a freely available, psychometrically sound, multiple-choice instrument to measure college students’ scientific literacy skill development. The research and development of the TOSLS is described in the journal CBE Life Sciences Education (http://www.lifescied.org/content/11/4/364.full) and has recently been highlighted as an Editor’s Choice article in the journal Science (see below).

From Science January 18, 2013:

Editors Choice – EDUCATION
Assessing Literacy
Melissa McCartney

Scientific literacy, a skill needed beyond the classroom, is being integrated into general education curriculums, resulting in a need to assess students as they develop scientific literacy skills. Gormally et al. describe the development of the Test of Scientific Literacy Skills (TOSLS) as a freely available, time-efficient, and psychometrically sound test for use in undergraduate introductory science courses. Using definitions of scientific literacy in education policy documents and survey results from general education faculty, the team identified two major skill categories as measurable outcomes, or TOSLS skills: recognizing and analyzing the use of methods of inquiry, and organizing, analyzing, and interpreting quantitative data. An extensive pilot study that included testing students in a general biology course, individual student interviews, and several rounds of expert faculty evaluation suggested that the TOSLS is able to identify students' scientific literacy skill proficiency. Additionally, the TOSLS was sensitive enough to detect pre- to post-semester learning gains, suggesting that it will be valuable in future assessment efforts. The full list of editor’s choice articles can be found at (http://www.sciencemag.org/content/339/6117/twil.full#compilation-1-4-art...).

In what is believed to be the first study of its kind, researchers used genomic techniques to document the presence of significant numbers of living microorganisms – principally bacteria – in the middle and upper troposphere, that section of the atmosphere approximately four to six miles above the Earth’s surface.

Whether the microorganisms routinely inhabit this portion of the atmosphere – perhaps living on carbon compounds also found there – or whether they were simply lofted there from the Earth’s surface isn’t yet known. The finding is of interest to atmospheric scientists, because the microorganisms could play a role in forming ice that may impact weather and climate. Long-distance transport of the bacteria could also be of interest for disease transmission models.

The microorganisms were documented in air samples taken as part of NASA’s Genesis and Rapid Intensification Processes (GRIP) program to study low- and high-altitude air masses associated with tropical storms. The sampling was done from a DC-8 aircraft over both land and ocean, including the Caribbean Sea and portions of the Atlantic Ocean. The sampling took place before, during and after two major tropical hurricanes – Earl and Karl – in 2010.

The research, which has been supported by NASA and the National Science Foundation, was published online January 28th by the journal Proceedings of the National Academy of Sciences.

“We did not expect to find so many microorganisms in the troposphere, which is considered a difficult environment for life,” said Kostas Konstantinidis, an assistant professor in the School of Civil and Environmental Engineering at the Georgia Institute of Technology. “There seems to be quite a diversity of species, but not all bacteria make it into the upper troposphere.”

Aboard the aircraft, a filter system designed by the research team collected particles – including the microorganisms – from outside air entering the aircraft’s sampling probes. The filters were analyzed using genomic techniques including polymerase chain reaction (PCR) and gene sequencing, which allowed the researchers to detect the microorganisms and estimate their quantities without using conventional cell-culture techniques.

When the air masses studied originated over the ocean, the sampling found mostly marine bacteria. Air masses that originated over land had mostly terrestrial bacteria. The researchers also saw strong evidence that the hurricanes had a significant impact on the distribution and dynamics of microorganism populations.

The study showed that viable bacterial cells represented, on average, around 20 percent of the total particles detected in the size range of 0.25 to 1 microns in diameter. By at least one order of magnitude, bacteria outnumbered fungi in the samples, and the researchers detected 17 different bacteria taxa – including some that are capable of metabolizing the carbon compounds that are ubiquitous in the atmosphere – such as oxalic acid.

The microorganisms could have an impact on cloud formation by supplementing (or replacing) the abiotic particles that normally serve as nuclei for forming ice crystals, said Athanasios Nenes, a professor in the Georgia Tech School of Earth and Atmospheric Sciences and School of Chemical and Biomolecular Engineering.

“In the absence of dust or other materials that could provide a good nucleus for ice formation, just having a small number of these microorganisms around could facilitate the formation of ice at these altitudes and attract surrounding moisture,” Nenes said. “If they are the right size for forming ice, they could affect the clouds around them.”

The microorganisms likely reach the troposphere through the same processes that launch dust and sea salt skyward. “When sea spray is generated, it can carry bacteria because there are a lot of bacteria and organic materials on the surface of the ocean,” Nenes said.

The research brought together microbiologists, atmospheric modelers and environmental researchers using the latest technologies for studying DNA. For the future, the researchers would like to know if certain types of bacteria are more suited than others for surviving at these altitudes. The researchers also want to understand the role played by the microorganisms – and determine whether or not they are carrying on metabolic functions in the troposphere.

“For these organisms, perhaps, the conditions may not be that harsh,” said Konstantinidis. “I wouldn’t be surprised if there is active life and growth in clouds, but this is something we cannot say for sure now.”

Other researchers have gathered biological samples from atop mountains or from snow samples, but gathering biological material from a jet aircraft required a novel experimental setup. The researchers also had to optimize protocols for extracting DNA from levels of biomass far lower than what they typically study in soils or lakes.

“We have demonstrated that our technique works, and that we can get some interesting information,” Nenes said. “A big fraction of the atmospheric particles that traditionally would have been expected to be dust or sea salt may actually be bacteria. At this point we are just seeing what’s up there, so this is just the beginning of what we hope to do.”

The Georgia Tech team also included Natasha DeLeon-Rodriguez and Luis-Miguel Rodriguez-R from the Georgia Tech School of Biology, Terry Lathem from the Georgia Tech School of Earth and Atmospheric Sciences, and James Barazesh and Michael Bergin from the Georgia Tech School of Civil and Environmental Engineering. The Georgia Tech team received assistance from researchers Bruce Anderson, Andreas Beyersdorf, and Luke Ziemba with the Chemistry and Dynamics Branch/Science Directorate at the NASA Langley Research Center in Hampton, Va.

CITATION: Natasha DeLeon-Rodriguez, et al., “Microbiome of the upper troposphere: Species composition and prevalence, effects of tropical storms, and atmospheric implications,” Proceedings of the National Academy of Sciences (2013): www.pnas.org/cgi/doi/10.1073/pnas.1212089110

This research was supported, in part, by NASA grant number NNX10AM63G, by a GAANN Fellowship from the U.S. Department of Education, a NASA-NESSF fellowship, and by a National Science Foundation (NSF) graduate research fellowship. The opinions expressed are those of the authors and do not necessarily represent the official views of NASA, the Department of Education or the NSF.

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Sand-dwelling and rock-dwelling cichlids living in East Africa’s Lake Malawi share a nearly identical genome, but have very different personalities. The territorial rock-dwellers live in communities where social interactions are important, while the sand-dwellers are itinerant and less aggressive.

Those behavioral differences likely arise from a complex region of the brain known as the telencephalon, which governs communication, emotion, movement and memory in vertebrates – including humans, where a major portion of the telencephalon is known as the cerebral cortex. A study published this week in the journal Nature Communications shows how the strength and timing of competing molecular signals during brain development has generated natural and presumably adaptive differences in the telencephalon much earlier than scientists had previously believed.

In the study, researchers first identified key differences in gene expression between rock- and sand-dweller brains during development, and then used small molecules to manipulate developmental pathways to mimic natural diversity.

“We have shown that the evolutionary changes in the brains of these fishes occur really early in development,” said Todd Streelman, an associate professor in the School of Biology and the Petit Institute for Bioengineering and Biosciences at the Georgia Institute of Technology. “It’s generally been thought that early development of the brain must be strongly buffered against change. Our data suggest that rock-dweller brains differ from sand-dweller brains – before there is a brain.”

For humans, the research could lead scientists to look for subtle changes in brain structures earlier in the development process. This could provide a better understanding of how disorders such as autism and schizophrenia could arise during very early brain development.

The research was supported by the National Science Foundation and published online April 23 by the journal.

“We want to understand how the telencephalon evolves by looking at genetics and developmental pathways in closely-related species from natural populations,” said Jonathan Sylvester, a postdoctoral researcher in the Georgia Tech School of Biology and lead author of the paper. “Adult cichlids have a tremendous amount of variation within the telencephalon, and we investigated the timing and cause of these differences. Unlike many previous studies in laboratory model organisms that focus on large, qualitative effects from knocking out single genes, we demonstrated that brain diversity evolves through quantitative tuning of multiple pathways.”

In examining the fish from embryos to adulthood, the researchers found that the mbuna, or rock-dwellers, tended to exhibit a larger ventral portion of the telencephalon, called the subpallium – while the sand-dwellers tended to have a larger version of the dorsal structure known as the pallium. These structures seem to have evolved differently over time to meet the behavioral and ecological needs of the fishes. The team showed that early variation in the activity of developmental signals expressed as complementary dorsal-ventral gradients, known technically as “Wingless” and “Hedgehog,” are involved in creating those differences during the neural plate stage, as a single sheet of neural tissue folds to form the neural tube.  

To specifically manipulate those two pathways, Sylvester removed clutches of between 20 and 40 eggs from brooding female cichlids, which normally incubate fertilized eggs in their mouths. At about 36 to 48 hours after fertilization, groups of eggs were exposed to small-molecule chemicals that either strengthened or weakened the Hedgehog signal, or strengthened or weakened the Wingless signal. The chemical treatment came while the structures that would become the brain were little more than a sheet of cells. After treatment, water containing the chemicals was replaced with fresh water, and the embryos were allowed to continue their development.

“We were able to artificially manipulate these pathways in a way that we think evolution might have worked to shift the process of rock-dweller telencephalon development to sand-dweller development, and vice-versa. Treatment with small molecules allows us incredible temporal and dose precision in manipulating natural development,” Sylvester explained. “We then followed the development of the embryos until we were able to measure the anatomical structures – the size of the pallium and subpallium – to see that we had transformed one to the other.”

The two different brain regions, the dorsal pallium and ventral subpallium, give rise to excitatory and inhibitory neurons in the forebrain. Altering the relative sizes of these regions might change the balance between these neuronal types, ultimately producing behavioral changes in the adult fish.

“Evolution has fine-tuned some of these developmental mechanisms to produce diversity,” Streelman said. “In this study, we have figured out which ones.”

The researchers studied six different species of East African cichlids, and also worked with collaborators at King’s College in London to apply similar techniques in the zebrafish.

As a next step, the researchers would like to follow the embryos through to adulthood to see if the changes seen in embryonic and juvenile brain structures actually do change behavior of adults. It’s possible, said Streelman, that later developmental events could compensate for the early differences.

The results could be of interest to scientists investigating human neurological disorders that result from an imbalance between excitatory and inhibitory neurons. Those disorders include autism and schizophrenia. “We think it is particularly interesting that there may be some adaptive variation in the natural proportions of excitatory versus inhibitory neurons in the species we study, correlated with their natural behavioral differences,” said Streelman.

In addition to the researchers already mentioned, the study included undergraduate coauthors Constance Rich and Chuyong Yi from Georgia Tech, and Joao Peres and Corinne Houart from King’s College in London. Rich is presently in the neuroscience PhD program at the University of Cambridge.

This research was supported by the National Science Foundation (NSF) under grants IOS 0922964 and IOS 1146275. The findings and conclusions are those of the authors and do not necessarily represent the official views of the NSF.

CITATION: Sylvester, J.B., et al., “Competing Signals Drive Telencephalon Diversity,” (Nature Communications, 2013).

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Ryan Bloomquist, the School of Biology’s first joint doctoral DMD/PhD student has received a F30 Ruth L. Kirschstein National Research Service Award (NRSA) aimed at investigating the process of dental tissue regeneration. The F30 Ruth L. Kirschstein NRSA is awarded to promising applicants with the potential to become productive, independent and highly trained physician-scientists.

Regenerative medicine, the general process of replacing or regenerating human cells and tissues to restore normal function, is emerging as a promising therapeutic strategy to address a wide array of congenital, traumatic and infectious diseases. On the forefront of these strategies is the field of regenerative dentistry, whereby cells or cell scaffolds are transplanted into oral tissues with the aim of culturing new teeth to restore ideal dental function and aesthetic. Although regenerative dentistry has been studied for many years, relatively little is known about how we naturally replace our teeth, including the identity of developmental precursor cells that give rise to new teeth.

Under the direction of Associate Professor Todd Streelman, Bloomquist seeks to exploit the continuously replaced dentition of the Lake Malawi cichlid fish to reveal the cells responsible for vertebrate tooth regeneration. Much like sharks and many other vertebrates, Lake Malawi cichlid fish from East Africa continuously replace their teeth throughout their lifetimes – making them ideal for studying dental regeneration. Beyond its direct application to regenerative dentistry, Bloomquist and Streelman hope to gain further insight on the general process of tissue regeneration that may contribute key insights for regenerative biology and engineering.

Bloomquist is completing a doctorate in Dental Medicine (DMD) at Georgia Regents University School of Dentistry and a PhD in Biology at Georgia Tech. He is the first student in either university to receive the prestigious F30 Ruth L. Kirschstein fellowship.

Using underwater video cameras to record fish feeding on South Pacific coral reefs, scientists have found that herbivorous fish can be picky eaters – a trait that could spell trouble for endangered reef systems.

In a study done at the Fiji Islands, the researchers learned that just four species of herbivorous fish were primarily responsible for removing common and potentially harmful seaweeds on reefs – and that each type of seaweed is eaten by a different fish species. The research demonstrates that particular species, and certain mixes of species, are potentially critical to the health of reef systems.

Related research also showed that even small marine protected areas – locations where fishing is forbidden – can encourage reef recovery.

“Of the nearly 30 species of bigger herbivores on the reef, there were four that were doing almost all of the feeding on the seven species of seaweeds that we studied,” said Mark Hay, a professor in the School of Biology at the Georgia Institute of Technology. “We did not see much overlap in the types of seaweed that each herbivore ate. Therefore, if any one of these four species was removed, that would potentially allow some macroalgae to proliferate.”

The research has been published online ahead of print by the journal Ecology and will be included in a future print edition. The study was supported by the National Science Foundation (NSF), the National Institutes of Health (NIH) and the Teasley Endowment to Georgia Tech.

Macroalgae – known as seaweeds – pose a major threat to endangered coral reefs. Some seaweeds emit chemicals that are toxic to corals, while others smother or abrade corals. If seaweed growth is not kept in check by herbivorous fish, the reefs can experience rapid decline. Overfishing of coral reef ecosystems has decimated fish populations in many areas, contributing to overgrowth by seaweed, along with the loss of corals and their ability to recover from disturbance.

To determine which fish were most important – information potentially useful for protecting them – Hay and Georgia Tech graduate student Douglas Rasher moved samples of seven species of seaweed into healthy reef systems that had large populations of fish.

They set up three video cameras to watch the reef areas, then left the area to allow the fish to feed. They repeated the experiment over a period of five days in three different marine protected areas located off the Fiji Islands. In all, Rasher watched more than 45 hours of video to carefully record which species of fish ate which species of seaweed.

“The patterns were remarkably consistent among the reefs in terms of which fish were responsible for removing the seaweed,” said Rasher. “Because different seaweeds use different defense strategies to deter herbivores from eating them, a particular mix of fish – each adapted to a particular type of seaweed – is needed to keep seaweeds off the reef.”

Among the most important were two species of unicornfish, which removed numerous types of brown algae. A species of parrotfish consumed red seaweeds, while a rabbitfish ate a type of green seaweed that is particularly toxic to coral. Those four fish species were responsible for 97 percent of the bites taken from all the seaweeds.

“It’s not enough to have herbivorous fish on the reef,” said Hay, who holds the Harry and Linda Teasley Chair in Environmental Biology at Georgia Tech. “We need to have the right mix of herbivores.”

While just four fish species consumed the large seaweeds, Rasher observed a different set of species involved in what he termed “maintenance” – the removal of small algal growths before they have a chance to grow.

“Through our videos, we were able to observe both groups in action,” he said. “There was not only little overlap in which fishes ate the large seaweeds, but there was also little overlap between fishes that comprised the two groups.”

To help determine why certain fish ate certain seaweed, the researchers played a trick on the unicornfish. They removed chemicals from each seaweed species that the unicornfish avoided and coated them individually on a species of seaweed that the unicornfish were accustomed to eating. That caused the fish to stop eating the chemical-laced seaweed, suggesting that chemical defenses kept them from consuming some seaweeds.

The researchers also compared the quality of coral reefs in marine protected areas to those in areas where fishing has been allowed. There are an estimated 300 marine protected areas in the Fiji Islands, most governed by local villages that have considerable autonomy over reef management.

Surveying these larger areas, the researchers found strong negative associations between the abundance or diversity of seaweed on the reef and diversity of herbivorous fishes at the sites they studied.

They found that strict rules against fishing in certain protected areas had led to a regeneration of corals, and that the contrast to fished areas nearby – some just 500 meters apart – was dramatic. The protected reefs supported as much as 11 times more live coral cover, 17 times more herbivorous fish biomass and three times more species diversity among herbivorous fishes as the unprotected areas.

“What we noted in Fiji is that where reefs are fished, they look like the devastated reefs in the Caribbean,” said Hay. “There’s a lot of seaweed, there’s almost no coral and there aren’t many fish in these flattened areas. But right next to them, where fishing hasn’t been allowed for the past eight or ten years, the reefs have recovered and have high coral cover, almost no seaweed and lots of fish.”

Although both fished and protected areas had only seven percent coral cover ten years ago, today the protected areas have recovered.

“This really demonstrates the value of reef protection, even on small scales,” Rasher said. “There is a lot of debate about whether or not small reserves work. This seems to be a nice example of an instance where they do.”

Ultimately, the researchers hope to provide information to village leaders that could help them manage their reefs to ensure long-term health – while helping feed the local human population.

“Not fishing is really not an option for people in these communities,” Rasher said. “Giving the village leadership an idea of which species are essential to reef health and what they can do to manage fisheries effectively is something we can do to help them maintain a sustainable reef food system.”

Beyond the researchers already mentioned, the research also included Andrew Hoey from the ARC Centre of Excellence for Coral Reef Studies at James Cook University in Townsville, Australia.

This research was supported by the National Science Foundation (NSF) under grants OCE 0929119 and DGE 0114400, and by the National Institutes of Health (NIH) under grant U01-TW007401. The opinions expressed are those of the authors and do not necessarily represent the official views of the NSF or NIH.

CITATION: Rasher, D.B. et al., Consumer diversity interacts with prey defenses to drive ecosystem function,” Ecology (2013): http://dx.doi.org/10.1890/12-0389.1

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When a shark is spotted in the ocean, humans and marine animals alike usually flee. But not the remora – this fish will instead swim right up to a shark and attach itself to the predator using a suction disk located on the top of its head. While we know why remoras attach to larger marine animals – for transportation, protection and food – the question of how they attach and detach from hosts without appearing to harm them remains unanswered.

A new study led by researchers at the Georgia Tech Research Institute (GTRI) provides details of the structure and tissue properties of the remora’s unique adhesion system. The researchers plan to use this information to create an engineered reversible adhesive inspired by the remora that could be used to create pain- and residue-free bandages, attach sensors to objects in aquatic or military reconnaissance environments, replace surgical clamps and help robots climb.

“While other creatures with unique adhesive properties – such as geckos, tree frogs and insects – have been the inspiration for laboratory-fabricated adhesives, the remora has been overlooked until now,” said GTRI senior research engineer Jason Nadler. “The remora’s attachment mechanism is quite different from other suction cup-based systems, fasteners or adhesives that can only attach to smooth surfaces or cannot be detached without damaging the host.”

The study results were presented at the Materials Research Society’s 2012 Fall Meeting and will be published in the meeting’s proceedings. The research was supported by the Georgia Research Alliance and GTRI.

The remora’s suction plate is a greatly evolved dorsal fin on top of the fish’s body. The fin is flattened into a disk-like pad and surrounded by a thick, fleshy lip of connective tissue that creates the seal between the remora and its host. The lip encloses rows of plate-like structures called lamellae, from which perpendicular rows of tooth-like structures called spinules emerge. The intricate skeletal structure enables efficient attachment to surfaces including sharks, sea turtles, whales and even boats.

To better understand how remoras attach to a host, Nadler and GTRI research scientist Allison Mercer teamed up with researchers from the Georgia Tech School of Biology and Woodruff School of Mechanical Engineering to investigate and quantitatively analyze the structure and form of the remora adhesion system, including its hierarchical nature.

Remora typically attach to larger marine animals for three reasons: transportation – a free ride that allows the remora to conserve energy; protection – being attacked when attached to a shark is unlikely; and food – sharks are very sloppy eaters, often leaving plenty of delectable morsels floating around for the remora to gobble up.

But whether this attachment was active or passive had been unclear. Results from the GTRI study suggest that remoras utilize a passive adhesion mechanism, meaning that the fish do not have to exert additional energy to maintain their attachment. The researchers suspect that drag forces created as the host swims actually increase the strength of the adhesion.

Dissection experiments showed that the remora’s attachment or release from a host could be controlled by muscles that raise or lower the lamellae. Dissection also revealed light-colored muscle tissue surrounding the suction disk, indicating low levels of myoglobin. For the remora to maintain active muscle control while attached to a marine host over long distances, the muscle tissue should display high concentrations of myoglobin, which were only seen in the much darker swimming muscles.

“We were very excited to discover that the adhesion is passive,” said Mercer. “We may be able to exploit and improve upon some of the adhesive properties of the fish to produce a synthetic material.”

The researchers also developed a technique that allowed them to collect thousands of measurements from three remora specimens, which yielded new insight into the shape, arrangement and spacing of their features. First, they imaged the remoras in attached and detached states using microtomography, optical microscopy and scanning electron microscopy. From the images, the researchers digitally reconstructed each specimen, measured characteristic features, and quantified structural similarities among specimens with significant size differences.

Detailed microtomography-based surface renderings of the lamellae showed a row of shorter, more regularly spaced and more densely packed spinules and another row of longer, less densely spaced spinules. A quantitative analysis uncovered similarities in suction disk structure with respect to the size and position of the lamellae and spinules despite significant specimen size differences. One of the fish’s disks was more than twice as long as the others, but the researchers observed a length-to-width ratio of each specimen’s adhesion disk that was within 16 percent of the average.

Through additional experiments, the researchers found that the spacing between the spinules on the remoras and the spacing between scales on mako sharks was remarkably similar.

“Complementary spacing between features on the remora and a shark likely contributes to the larger adhesive strength that has been observed when remoras are attached to shark skin compared to smoother surfaces,” said Mercer.

The researchers are planning to conduct further tests to better understand the roles of the various suction disk structural elements and their interactions to create a successful attachment and detachment system in the laboratory.

“We are not trying to replicate the exact remora adhesion structure that occurs in nature,” explained Nadler. “We would like to identify, characterize and harness its critical features to design and test attachment systems that enable those unique adhesive functions. Ultimately, we want to optimize a bio-inspired adhesive for a wide variety of applications that have capabilities and performance advantages over adhesives or fasteners available today.”

In addition to those already mentioned, the following researchers also contributed to this work: Georgia Tech mechanical engineering research engineer Angela Lin, professor Robert Guldberg and graduate student Michael Culler; Georgia Tech biology graduate student Ryan Bloomquist and associate professor Todd Streelman; GTRI research scientist Keri Ledford, and Georgia Aquarium Director of Research and Conservation Dr. Alistair Dove.

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On April 24th, graduating seniors gathered with Biology faculty, researchers, and other students to present and celebrate their undergraduate research projects. Biology majors at Georgia Tech are required to complete a senior research experience in which they conduct an individual research project mentored by a faculty member or participate in a group research project undertaken as part of the Research Project Lab course. Several Biology majors also completed the Research Option this year, following multiple semesters of research effort and the preparation of an undergraduate thesis. This year, Georgia Tech President Bud Peterson and Provost Rafael Bras attended the poster session to congratulate our seniors and learn about their scientific accomplishments.

Future teams of subterranean search and rescue robots may owe their success to the lowly fire ant, a much despised insect whose painful bites and extensive networks of underground tunnels are all-too-familiar to people living in the southern United States.

• Watch a YouTube video of this project.

By studying fire ants in the laboratory using video tracking equipment and X-ray computed tomography, researchers have uncovered fundamental principles of locomotion that robot teams could one day use to travel quickly and easily through underground tunnels. Among the principles is building tunnel environments that assist in moving around by limiting slips and falls, and by reducing the need for complex neural processing.

Among the study’s surprises was the first observation that ants in confined spaces use their antennae for locomotion as well as for sensing the environment.

“Our hypothesis is that the ants are creating their environment in just the right way to allow them to move up and down rapidly with a minimal amount of neural control,” said Daniel Goldman, an associate professor in the School of Physics at the Georgia Institute of Technology, and one of the paper’s co-authors. “The environment allows the ants to make missteps and not suffer for them. These ants can teach us some remarkably effective tricks for maneuvering in subterranean environments.”

The research was reported May 20 in the early edition of the journal Proceedings of the National Academy of Sciences. The work was sponsored by the National Science Foundation’s Physics of Living Systems program.

In a series of studies carried out by graduate research assistant Nick Gravish, groups of fire ants (Solenopsis invicta) were placed into tubes of soil and allowed to dig tunnels for 20 hours. To simulate a range of environmental conditions, Gravish and postdoctoral fellow Daria Monaenkova varied the size of the soil particles from 50 microns on up to 600 microns, and also altered the moisture content from 1 to 20 percent.

While the variations in particle size and moisture content did produce changes in the volume of tunnels produced and the depth that the ants dug, the diameters of the tunnels remained constant – and comparable to the length of the creatures’ own bodies: about 3.5 millimeters.

“Independent of whether the soil particles were as large as the animals’ heads or whether they were fine powder, or whether the soil was damp or contained very little moisture, the tunnel size was always the same within a tight range,” said Goldman. “The size of the tunnels appears to be a design principle used by the ants, something that they were controlling for.”

Gravish believes such a scaling effect allows the ants to make best use of their antennae, limbs and body to rapidly ascend and descend in the tunnels by interacting with the walls and limiting the range of possible missteps.

“In these subterranean environments where their leg motions are certainly hindered, we see that the speeds at which these ants can run are the same,” he said. “The tunnel size seems to have little, if any, effect on locomotion as defined by speed.”

The researchers used X-ray computed tomography to study tunnels the ants built in the test chambers, gathering 168 observations. They also used video tracking equipment to collect data on ants moving through tunnels made between two clear plates – much like “ant farms” sold for children – and through a maze of glass tubes of differing diameters.

The maze was mounted on an air piston that was periodically fired, dropping the maze with a force of as much as 27 times that of gravity. The sudden movement caused about half of the ants in the tubes to lose their footing and begin to fall. That led to one of the study’s most surprising findings: the creatures used their antennae to help grab onto the tube walls as they fell.

“A lot of us who have studied social insects for a long time have never seen antennae used in that way,” said Michael Goodisman, a professor in the Georgia Tech School of Biology and one of the paper’s other co-authors. “It’s incredible that they catch themselves with their antennae. This is an adaptive behavior that we never would have expected.”

By analyzing ants falling in the glass tubes, the researchers determined that the tube diameter played a key role in whether the animals could arrest their fall.

In future studies, the researchers plan to explore how the ants excavate their tunnel networks, which involves moving massive amounts of soil. That soil is the source of the large mounds for which fire ants are known.

While the research focused on understanding the principles behind how ants move in confined spaces, the results could have implications for future teams of small robots.

“The problems that the ants face are the same kinds of problems that a digging robot working in a confined space would potentially face – the need for rapid movement, stability and safety – all with limited sensing and brain power,” said Goodisman. “If we want to build machines that dig, we can build in controls like these ants have.”  

Why use fire ants for studying underground locomotion?

“These animals dig virtually non-stop, and they are good, repeatable study subjects,” Goodisman explained. “And they are very convenient for us to study. We can go outside the laboratory door and collect them virtually anywhere.”

The research described here has been sponsored by the National Science Foundation (NSF) under grant POLS 095765, and by the Burroughs Wellcome Fund. The findings and conclusions are those of the authors and do not necessarily represent the official views of the NSF.

CITATION: Nick Gravish, et al., “Climbing, falling and jamming during ant locomotion in confined environments,” (Proceedings of the National Academy of Sciences, 2013).

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A new study of both computer-created and natural proteins suggests that the number of unique pockets – sites where small molecule pharmaceutical compounds can bind to proteins – is surprisingly small, meaning drug side effects may be impossible to avoid. The study also found that the fundamental biochemical processes needed for life could have been enabled by the simple physics of protein folding.  

Studying a set of artificial proteins and comparing them to natural proteins, researchers at the Georgia Institute of Technology have concluded that there may be no more than about 500 unique protein pocket configurations that serve as binding sites for small molecule ligands. Therefore, the likelihood that a molecule intended for one protein target will also bind with an unintended target is significant, said Jeffrey Skolnick, a professor in the School of Biology at Georgia Tech.

“Our study provides a rationalization for why a lot of drugs have significant side effects – because that is intrinsic to the process,” said Skolnick. “There are only a relatively small number of different ligand binding pockets. The likelihood of having geometry in an amino acid composition that will bind the same ligand turns out to be much higher than anyone would have anticipated. This means that the idea that a small molecule could have just one protein target can’t be supported.”

Research on the binding pockets was published May 20 in the early edition of the journal Proceedings of the National Academy of Sciences. The research was supported by the National Institutes of Health (NIH).

Skolnick and collaborator Mu Gao have been studying the effects of physics on the activity of protein binding, and contrasting the original conditions created by the folding of amino acid residues against the role played by evolution in optimizing the process.

“The basic physics of the system provides the mechanism for molecules to bind to proteins,” said Skolnick, who is director of the Center for the Study of Systems Biology at Georgia Tech. “You don’t need evolution to have a system that works on at least a low level. In other words, proteins are inherently capable of engaging in biochemical function without evolution’s selection. Beyond unintended drug effects, this has a lot of implications for the biochemical component of the origins of life.”

Binding pockets on proteins are formed by the underlying secondary structure of the amino acids, which is directed by hydrogen bonding in the chemistry. That allows formation of similar pockets on many different proteins, even those that are not directly related to one another.

“You could have the same or very similar pockets on the same protein, the same pockets on similar proteins, and the same pockets on completely dissimilar proteins that have no evolutionary relationship. In proteins that are related evolutionarily or that have similar structures, you could have very dissimilar pockets,” said Skolnick, who is also a Georgia Research Alliance Eminent Scholar. “This helps explain why we see unintended effects of drugs, and opens up a new paradigm for how one has to think about discovering drugs.”

The implications of this “biochemical noise” for the drug discovery process could be significant. To counter the impact of unintended effects, drug developers will need to know more about the available pockets so they can avoid affecting binding locations that are also located on proteins critical to life processes. If the inevitable unintended binding takes place on less critical proteins, the side effects may be less severe.

In addition, drug development could also move to a higher level, examining the switches that modulate the activity of proteins beyond binding sites. That may require a different approach to drug development.

“The strategy for minimizing side effects and maximizing positive effects may have to operate at a higher level,” Skolnick said. “You are never going to be able to design unintended binding effects away. But you can minimize the undesirable effects to some extent.”

In their study, Skolnick and Gao used computer simulations to produce a series of artificial proteins that were folded according the laws of physics, but not optimized for function. Using an algorithm that compares pairs of pockets and assesses the statistical significance of their structural overlap, they analyzed the similarity between the binding pockets in the artificial proteins and the pockets on a series of native proteins. The artificial pockets all had corresponding pockets on the natural proteins, suggesting that the simple physics of folding has been a major factor in development of the pockets.

“This is how life, at least the biochemistry of life, could have gotten started,” said Skolnick. “Evolution would have optimized the functions, but you don’t need that to get started at a low level of efficiency. If you had a soup of our artificial proteins, even with no selection you could at least do low-level biochemistry.”

Though the basic biochemistry of life was made possible by simple physics, optimizing the binding process to allow the efficiencies seen in modern organisms would have required evolutionary selection.

“This is the first time that it has been shown that side effects of drugs are an inherent, fundamental property of proteins rather than a property that can be controlled for in the design,” Skolnick added. “The physics involved is more important than had been generally appreciated.

Research reported in this news release was supported by the Institute of General Medical Sciences of the National Institutes of Health (NIH) under award number GM48835. The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.

CITATION: Jeffrey Skolnick and Mu Gao, “Interplay of physics and evolution in the likely origin of protein biochemical function,” (Proceedings of the National Academy of Sciences, 2013).

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Eric Gaucher, associate professor in Georgia Tech's School of Biology, was named as one of 14 young faculty from seven nations to receive an early career grant by DuPont. The DuPont Young Professor program is designed to help promising young and untenured research faculty begin their research careers.The $75,000 award is unrestricted and not tied to a specific research project.

"It is a wonderful honor to receive this award because, in many regards, it is a validation that there is utility associated with our research," said Gaucher. "This is also validation for Georgia Tech because it demonstrates that the Institute has been successful in fostering the development of research and technology that reaches beyond the academic environment."

Gaucher came to Tech in 2008 with a Ph.D. in evolutionary and biomedical sciences from the University of Florida. His research is focused on understanding the origins and evolution of life on earth. Last year, Gaucher's lab resurrected a 500-million-year-old gene from a bacterium and inserted it into a modern bacterium, Escherichia coli (E. coli). As a result they've been able to watch how the gene evolves.

"Our research exploits a unique protein-engineering platform of interest to DuPont because recombinant proteins have become extremely prevalent throughout society yet we desperately need new ways to improve how such proteins are engineered and developed," said Gaucher. "We will use the money associated with this award to validate that our platform is useful to diverse sectors such as bioindustry, agriculture and biomedicine."

Since 1968, DuPont has provided nearly $50 million in grants to more than 680 young professors in more than 130 institutions in 14 countries. In addition to providing unrestricted funding to new faculty, this prestigious program enables DuPont to build future research partnerships with emerging, global academic leaders.

Research interests within the class of 2013 Young Professors represent key components of DuPont science and include promising research in the fields of: environmental remediation, genomic prediction, optics in nanoscience, pest management, phytochemicals for nutrition and medicine, plant breeding, protein engineering, studies of the human microbiome, sustainable energy and fuel production, and, water treatment and desalinization.

Professors are nominated by a member of the DuPont technical staff and the nominator serves as the liaison between the company and the faculty member. During the three-year award, each grant recipient is invited to present a seminar on his or her work to the DuPont research community.